RESTful Open Annotation

RESTful Open Annotation (REST-OA) provides a simple API for sharing annotations online together with reference implementations and tools and resources implementing the API.

Specification

The formal specification of the RESTful Open Annotation API.

• Homepage: http://restful-open-annotation.github.io/spec

Reference implementation

Reference server and client implementations plus tools for format conversion and validation.

Store

Server-side annotation storage that allows clients to create, read, update and delete annotations using the API.

• Homepage: https://github.com/restful-open-annotation/eve-restoa
• Example: http://weaver.nlplab.org/api/annotations/1

Explorer

Client that provides an HTML interface for navigating and visualizing the contents of any compatible store.

• Homepage: http://weaver.nlplab.org:7000/explore
• Example: visualize CoNLL’02 document

Adapter

Middleware for sharing OA data. Implements both the client and server sides of the API and a conversions to and from different serializations of the OA model and related formats.

• Homepage: https://github.com/restful-open-annotation/oa-adapter

Validation

Support for OA JSON data validation is provided using JSON Schema.

• Homepage: https://github.com/restful-open-annotation/schema

Tools and resources

brat

brat rapid annotation tool is an open-source web-based annotation tool. Both the brat client and server implement experimental REST-OA support.

• Homepage: http://brat.nlplab.org

tagtog

tagtog is a web-based annotation system designed to combine manual and automatic annotations to accurately and efficiently mark up full-text articles. Both the tagtog client and server implement experimental REST-OA support.

• Homepage: https://www.tagtog.net/

Biomedical entity recognition resources

The COMPARTMENTS, TISSUES, DISEASES and ORGANISMS resources contain the results of entity recognition on the biomedical literature for the purpose of linking proteins to their subcellular localizations, the tissues in which they are involved, and the diseases they are associated with.

• Homepage: http://jensenlab.org/
• Example: visualize COMPARTMENTS annotations
• Example: visualize TISSUES annotations
• Example: visualize DISEASES annotations
• Example: visualize ORGANISMS annotations

EVEX

EVEX is a text mining resource that covers the entire publicly available biomedical literature and contains over 40 million bio-molecular events among more than 76 million automatically extracted gene/protein name mentions enriched with gene normalization results.

• Homepage: http://evexdb.org/
• Example: visualize EVEX annotations